Update on my top issue. My Crossfire mechanic ran a full diagnostic and discovered the PTCM is fried. I have no idea how that happened, but probably something I did!
Anyway, these modules are no longer stocked/manufactured by Chrysler. I found one on eBay, took the car back to my mechanic.
He had found number 7 fuse blown and had to clear the fault codes, but got the top working again. $ well worth it.
One lesson learned: always snap pics with your phone before taking things apart.